data_6GKM # _model_server_result.job_id RnriwhLZwaG1CIeqqrwU3g _model_server_result.datetime_utc '2025-03-06 07:08:03' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6gkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1102}' # _entry.id 6GKM # _exptl.entry_id 6GKM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6GKM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 889 A CYS 907 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc2 A SG CYS 892 A CYS 910 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc3 A SG CYS 944 A CYS 962 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 A SG CYS 946 A CYS 964 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? hydrog WATSON-CRICK hydrog1 B N3 C 1 X C 1 1_555 C N1 G 14 Y G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 1 X C 1 1_555 C O6 G 14 Y G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 1 X C 1 1_555 C N2 G 14 Y G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 A 2 X A 2 1_555 C N3 U 13 Y U 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 A 2 X A 2 1_555 C O4 U 13 Y U 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 A 3 X A 3 1_555 C N3 U 12 Y U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 A 3 X A 3 1_555 C O4 U 12 Y U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 G 4 X G 4 1_555 C N3 C 11 Y C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N2 G 4 X G 4 1_555 C O2 C 11 Y C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O6 G 4 X G 4 1_555 C N4 C 11 Y C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 C 5 X C 5 1_555 C N1 G 10 Y G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 C 5 X C 5 1_555 C O6 G 10 Y G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 C 5 X C 5 1_555 C N2 G 10 Y G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 C 6 X C 6 1_555 C N1 G 9 Y G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 C 6 X C 6 1_555 C O6 G 9 Y G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 C 6 X C 6 1_555 C N2 G 9 Y G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 G 7 X G 7 1_555 C N3 C 8 Y C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 G 7 X G 7 1_555 C O2 C 8 Y C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 G 7 X G 7 1_555 C N4 C 8 Y C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 A 8 X A 8 1_555 C N3 U 7 Y U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N6 A 8 X A 8 1_555 C O4 U 7 Y U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 G 9 X G 9 1_555 C N3 C 6 Y C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 G 9 X G 9 1_555 C O2 C 6 Y C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 G 9 X G 9 1_555 C N4 C 6 Y C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 G 10 X G 10 1_555 C N3 C 5 Y C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N2 G 10 X G 10 1_555 C O2 C 5 Y C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O6 G 10 X G 10 1_555 C N4 C 5 Y C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 A 11 X A 11 1_555 C N3 U 4 Y U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N6 A 11 X A 11 1_555 C O4 U 4 Y U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N1 G 12 X G 12 1_555 C N3 C 3 Y C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N2 G 12 X G 12 1_555 C O2 C 3 Y C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O6 G 12 X G 12 1_555 C N4 C 3 Y C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N1 A 13 X A 13 1_555 C N3 U 2 Y U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N6 A 13 X A 13 1_555 C O4 U 2 Y U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N1 G 14 X G 14 1_555 C N3 C 1 Y C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N2 G 14 X G 14 1_555 C O2 C 1 Y C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O6 G 14 X G 14 1_555 C N4 C 1 Y C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G ATP doub 109 n n PG O2G ATP sing 110 n n PG O3G ATP sing 111 n n PG O3B ATP sing 112 n n O2G HOG2 ATP sing 113 n n O3G HOG3 ATP sing 114 n n PB O1B ATP doub 115 n n PB O2B ATP sing 116 n n PB O3B ATP sing 117 n n PB O3A ATP sing 118 n n O2B HOB2 ATP sing 119 n n PA O1A ATP doub 120 n n PA O2A ATP sing 121 n n PA O3A ATP sing 122 n n PA O5' ATP sing 123 n n O2A HOA2 ATP sing 124 n n O5' C5' ATP sing 125 n n C5' C4' ATP sing 126 n n C5' "H5'1" ATP sing 127 n n C5' "H5'2" ATP sing 128 n n C4' O4' ATP sing 129 n n C4' C3' ATP sing 130 n n C4' H4' ATP sing 131 n n O4' C1' ATP sing 132 n n C3' O3' ATP sing 133 n n C3' C2' ATP sing 134 n n C3' H3' ATP sing 135 n n O3' HO3' ATP sing 136 n n C2' O2' ATP sing 137 n n C2' C1' ATP sing 138 n n C2' H2' ATP sing 139 n n O2' HO2' ATP sing 140 n n C1' N9 ATP sing 141 n n C1' H1' ATP sing 142 n n N9 C8 ATP sing 143 n y N9 C4 ATP sing 144 n y C8 N7 ATP doub 145 n y C8 H8 ATP sing 146 n n N7 C5 ATP sing 147 n y C5 C6 ATP sing 148 n y C5 C4 ATP doub 149 n y C6 N6 ATP sing 150 n n C6 N1 ATP doub 151 n y N6 HN61 ATP sing 152 n n N6 HN62 ATP sing 153 n n N1 C2 ATP sing 154 n y C2 N3 ATP doub 155 n y C2 H2 ATP sing 156 n n N3 C4 ATP sing 157 n y # _atom_sites.entry_id 6GKM _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 ZN A 1 1101 1099 ZN ZN . E 5 ATP A 1 1102 1101 ATP ATP . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG ATP . . . E 5 94.019 134.823 121.712 1 131.04 ? PG ATP 1102 A 1 HETATM 2 O O1G ATP . . . E 5 93.648 134.905 120.253 1 131.04 ? O1G ATP 1102 A 1 HETATM 3 O O2G ATP . . . E 5 95.165 135.705 122.16 1 131.04 ? O2G ATP 1102 A 1 HETATM 4 O O3G ATP . . . E 5 94.097 133.393 122.182 1 131.04 ? O3G ATP 1102 A 1 HETATM 5 P PB ATP . . . E 5 92.588 135.245 124.077 1 131.04 ? PB ATP 1102 A 1 HETATM 6 O O1B ATP . . . E 5 91.259 134.58 124.333 1 131.04 ? O1B ATP 1102 A 1 HETATM 7 O O2B ATP . . . E 5 93.866 134.643 124.603 1 131.04 ? O2B ATP 1102 A 1 HETATM 8 O O3B ATP . . . E 5 92.759 135.449 122.489 1 131.04 ? O3B ATP 1102 A 1 HETATM 9 P PA ATP . . . E 5 91.123 137.563 124.405 1 131.04 ? PA ATP 1102 A 1 HETATM 10 O O1A ATP . . . E 5 90.383 136.904 123.266 1 131.04 ? O1A ATP 1102 A 1 HETATM 11 O O2A ATP . . . E 5 91.493 139.02 124.295 1 131.04 ? O2A ATP 1102 A 1 HETATM 12 O O3A ATP . . . E 5 92.491 136.752 124.615 1 131.04 ? O3A ATP 1102 A 1 HETATM 13 O O5' ATP . . . E 5 90.341 137.331 125.786 1 131.04 ? O5' ATP 1102 A 1 HETATM 14 C C5' ATP . . . E 5 90.962 137.658 127.025 1 131.04 ? C5' ATP 1102 A 1 HETATM 15 C C4' ATP . . . E 5 90.135 138.79 127.61 1 131.04 ? C4' ATP 1102 A 1 HETATM 16 O O4' ATP . . . E 5 89.079 139.1 126.701 1 131.04 ? O4' ATP 1102 A 1 HETATM 17 C C3' ATP . . . E 5 89.514 138.393 128.934 1 131.04 ? C3' ATP 1102 A 1 HETATM 18 O O3' ATP . . . E 5 90.082 139.176 129.99 1 131.04 ? O3' ATP 1102 A 1 HETATM 19 C C2' ATP . . . E 5 88.037 138.687 128.806 1 131.04 ? C2' ATP 1102 A 1 HETATM 20 O O2' ATP . . . E 5 87.639 139.657 129.774 1 131.04 ? O2' ATP 1102 A 1 HETATM 21 C C1' ATP . . . E 5 87.851 139.254 127.413 1 131.04 ? C1' ATP 1102 A 1 HETATM 22 N N9 ATP . . . E 5 86.738 138.522 126.764 1 131.04 ? N9 ATP 1102 A 1 HETATM 23 C C8 ATP . . . E 5 86.816 137.43 125.985 1 131.04 ? C8 ATP 1102 A 1 HETATM 24 N N7 ATP . . . E 5 85.58 137.042 125.577 1 131.04 ? N7 ATP 1102 A 1 HETATM 25 C C5 ATP . . . E 5 84.695 137.904 126.109 1 131.04 ? C5 ATP 1102 A 1 HETATM 26 C C6 ATP . . . E 5 83.229 138.075 126.093 1 131.04 ? C6 ATP 1102 A 1 HETATM 27 N N6 ATP . . . E 5 82.462 137.207 125.394 1 131.04 ? N6 ATP 1102 A 1 HETATM 28 N N1 ATP . . . E 5 82.692 139.104 126.782 1 131.04 ? N1 ATP 1102 A 1 HETATM 29 C C2 ATP . . . E 5 83.46 139.95 127.494 1 131.04 ? C2 ATP 1102 A 1 HETATM 30 N N3 ATP . . . E 5 84.803 139.856 127.549 1 131.04 ? N3 ATP 1102 A 1 HETATM 31 C C4 ATP . . . E 5 85.462 138.858 126.909 1 131.04 ? C4 ATP 1102 A 1 # _model_server_stats.io_time_ms 99 _model_server_stats.parse_time_ms 114 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #